Psyllid ID: psy4559

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330------

MLTYVLRVWHLPISMGDRLGPHVEAISGSTFSKDSWLKSQRKDHKKINMTLLIKGWLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVDKMDPMRPQLQSVNMTDSDSTDGSNVSDGNRTVLET

ccEEEEEEEEcccccccccccccccccccccccccHHHHHHcccccccEEEEEHHHHHHHHccccEEEEEEEEccccccccEEEEEcccccHHHHHHHHHHHcccHHHHHHHHHcccccHHHHHHHHHHcccccccccccEEEEEEEEEEcccccccccccccccccHHHHHHHccccccEEEcccccccccccccHHHHHHHHccccccccccccEEEEEEEEEEcccEEEEEEEEccccHHHHHHHHHHHHHHccccEEEEEEEEEEEEccccccccccccccHHHHHHHHHccHHHHHccccccccccccccccccccccccccccccccccc

ccEEEEEEEEccccccccccccEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccHcHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccccccccccEEEEEEEEEcccccccHHHHHHHHcccHHHHHccccHHHHHHHHHcHHHcccccccHHHHHHHHcccccccccccEEEEEEEEEEccccEEEEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEEEccccccHHHHHHHHcccHHHHHHHHHHHHHHHccccHHHccccccEcccccccccccccccccEEEcc

MLTYVLRVWHlpismgdrlgphveaisgstfskdswlksqrkdhkKINMTLLIKGWLSYMKNKKNITVLVSLIDlfvpallpwqetvtvpsikpLQKVLKIidnnnclfvhrqagvrlnsqeaydvacqgpirpallkepvvyglkcvhfkppdftignLYSALLPWQEAVLKITDNNCLFVCLFVHrqagvrlnsqeaydiarqgpirpallkepvvyglkcvhfkppdftieVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIahnetlvdkmdpmrpqlqsvnmtdsdstdgsnvsdgnrtvlet

MLTYVLRVWHLPISMGDRLGPHVEAISgstfskdswlksqrkdhkkiNMTLLIKGWLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAhnetlvdkmdPMRPQLQSVnmtdsdstdgsnvsdgnrtvlet

**TYVLRVWHLPISMGDRLGPHVEAISGSTF***SWL******HKKINMTLLIKGWLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLV************************************

*LTYVLRVWHLPISMGDRLGPHVEAISGSTFSKDSWLKSQRKDHKKINMTLLIKGWLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSAL*PW*EAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVDKMDPM******************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		336	2.2.26 [Sep-21-2011]
Q5XGG2		325	Probable tRNA pseudouridi	yes	N/A	0.339	0.350	0.376	5e-20
Q91WG3		331	Probable tRNA pseudouridi	yes	N/A	0.297	0.302	0.39	3e-18
Q5XFW2		323	Probable tRNA pseudouridi	yes	N/A	0.297	0.309	0.39	4e-17
O95900		331	Probable tRNA pseudouridi	yes	N/A	0.297	0.302	0.35	3e-15
Q8WWH5		349	Probable tRNA pseudouridi	no	N/A	0.321	0.309	0.258	3e-05
Q8C0D0		338	Probable tRNA pseudouridi	no	N/A	0.372	0.369	0.230	0.0009

>sp\|Q5XGG2\|TRUB2_XENTR Probable tRNA pseudouridine synthase 2 OS=Xenopus tropicalis GN=trub2 PE=2 SV=1	Back alignment and function desciption

 Score = 99.0 bits (245), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 44/117 (37%), Positives = 74/117 (63%), Gaps = 3/117 (2%)

Query: 194 LNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLG 253
           L SQEAYD+A QG +RP +   P++ G++C+ F PP+FT+E+ C+ E +++L ++I+++G
Sbjct: 187 LQSQEAYDLAVQGKLRPMVKSPPIILGIRCLEFSPPEFTLEIQCMHETQQYLRKMIHEIG 246

Query: 254 TKLRSAAICTSIQCIRFAQFGLEHSLLRKHW---RVQHVIENIAHNETLVDKMDPMR 307
            +LRS+A+CT ++  R   F ++ SLLR  W    +Q  I         V + +P R
Sbjct: 247 LELRSSAVCTQVRRSRDGPFTVDCSLLRTQWDLGSIQGAIRECRAQTEGVSRGNPDR 303

May be responsible for synthesis of pseudouridine from uracil in transfer RNAs.
Xenopus tropicalis (taxid: 8364)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp\|Q91WG3\|TRUB2_MOUSE Probable tRNA pseudouridine synthase 2 OS=Mus musculus GN=Trub2 PE=2 SV=1	Back alignment and function description

>sp\|Q5XFW2\|TRUB2_RAT Probable tRNA pseudouridine synthase 2 OS=Rattus norvegicus GN=Trub2 PE=2 SV=1	Back alignment and function description

>sp\|O95900\|TRUB2_HUMAN Probable tRNA pseudouridine synthase 2 OS=Homo sapiens GN=TRUB2 PE=1 SV=1	Back alignment and function description

>sp\|Q8WWH5\|TRUB1_HUMAN Probable tRNA pseudouridine synthase 1 OS=Homo sapiens GN=TRUB1 PE=1 SV=1	Back alignment and function description

>sp\|Q8C0D0\|TRUB1_MOUSE Probable tRNA pseudouridine synthase 1 OS=Mus musculus GN=Trub1 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		336
91082291		304	PREDICTED: similar to AGAP002077-PA [Tri	0.348	0.384	0.512	3e-29
270007464		240	hypothetical protein TcasGA2_TC014046 [T	0.348	0.487	0.512	4e-29
357620125		306	hypothetical protein KGM_09344 [Danaus p	0.348	0.382	0.452	4e-27
321471521		328	hypothetical protein DAPPUDRAFT_302506 [	0.357	0.365	0.458	2e-26
241742049		325	conserved hypothetical protein [Ixodes s	0.383	0.396	0.396	3e-26
332374130		304	unknown [Dendroctonus ponderosae]	0.306	0.338	0.504	2e-25
193700133		316	PREDICTED: probable tRNA pseudouridine s	0.309	0.329	0.480	3e-25
350416125		321	PREDICTED: probable tRNA pseudouridine s	0.333	0.348	0.455	2e-24
332017988		317	Putative tRNA pseudouridine synthase 2 [	0.336	0.356	0.442	1e-23
340711427		298	PREDICTED: probable tRNA pseudouridine s	0.333	0.375	0.437	1e-23

>gi\|91082291\|ref\|XP_973881.1\| PREDICTED: similar to AGAP002077-PA [Tribolium castaneum]	Back alignment and taxonomy information

 Score =  135 bits (339), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/117 (51%), Positives = 86/117 (73%)

Query: 188 RQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIR 247
           +  G+ L S+EAY +A QGPIRPA  K PV+YG+KCV F+PP+F IE+ CI EYE +L  
Sbjct: 177 KSCGIDLQSEEAYKLACQGPIRPANSKLPVIYGIKCVKFEPPEFVIEIQCINEYETYLRS 236

Query: 248 LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVDKMD 304
           LI+++G KL S+A CT+IQCIR + F +E++LLRKHW +Q +I N+     ++D+ +
Sbjct: 237 LIHEIGMKLHSSAHCTAIQCIRHSYFTVENALLRKHWTLQDIITNMEQCIQIMDEHE 293

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|270007464\|gb\|EFA03912.1\| hypothetical protein TcasGA2_TC014046 [Tribolium castaneum]	Back alignment and taxonomy information

>gi\|357620125\|gb\|EHJ72431.1\| hypothetical protein KGM_09344 [Danaus plexippus]	Back alignment and taxonomy information

>gi\|321471521\|gb\|EFX82494.1\| hypothetical protein DAPPUDRAFT_302506 [Daphnia pulex]	Back alignment and taxonomy information

>gi\|241742049\|ref\|XP_002414158.1\| conserved hypothetical protein [Ixodes scapularis] gi\|215508012\|gb\|EEC17466.1\| conserved hypothetical protein [Ixodes scapularis]	Back alignment and taxonomy information

>gi\|332374130\|gb\|AEE62206.1\| unknown [Dendroctonus ponderosae]	Back alignment and taxonomy information

>gi\|193700133\|ref\|XP_001944222.1\| PREDICTED: probable tRNA pseudouridine synthase 2-like [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|350416125\|ref\|XP_003490850.1\| PREDICTED: probable tRNA pseudouridine synthase 2-like [Bombus impatiens]	Back alignment and taxonomy information

>gi\|332017988\|gb\|EGI58625.1\| Putative tRNA pseudouridine synthase 2 [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|340711427\|ref\|XP_003394277.1\| PREDICTED: probable tRNA pseudouridine synthase 2-like [Bombus terrestris]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		336
FB\|FBgn0033060		317	CG7849 [Drosophila melanogaste	0.380	0.403	0.387	7.8e-23
ZFIN\|ZDB-GENE-040704-41		352	trub2 "TruB pseudouridine (psi	0.422	0.403	0.371	4.3e-22
MGI\|MGI:2442186		331	Trub2 "TruB pseudouridine (psi	0.294	0.299	0.405	2.6e-17
RGD\|1359394		323	Trub2 "TruB pseudouridine (psi	0.288	0.300	0.42	3.7e-16
UNIPROTKB\|Q5XFW2		323	Trub2 "Probable tRNA pseudouri	0.288	0.300	0.42	3.7e-16
UNIPROTKB\|F1NEP1		318	TRUB2 "Uncharacterized protein	0.309	0.327	0.330	8.1e-16
UNIPROTKB\|B7Z7G5		275	TRUB2 "cDNA FLJ52131, highly s	0.294	0.36	0.366	2.7e-15
UNIPROTKB\|F1RR98		331	TRUB2 "Uncharacterized protein	0.288	0.293	0.4	1.3e-14
UNIPROTKB\|E2RSQ5		329	TRUB2 "Uncharacterized protein	0.288	0.294	0.4	3e-14
UNIPROTKB\|J9P6Q3		350	TRUB2 "Uncharacterized protein	0.288	0.277	0.4	4.1e-14

FB\|FBgn0033060 CG7849 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 50/129 (38%), Positives = 81/129 (62%)

Query:   191 GVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIY 250
             GV L +QEAY++A +G +RPA   +PVVYG+K +HF  P FT+E+H I E +E+L  L++
Sbjct:   190 GVDLQTQEAYELACRGLLRPADDSQPVVYGIKLIHFDRPHFTLELHAINETQEYLATLVH 249

Query:   251 DLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVDKMDPMRPQL 310
             D+   LR+ A C+ ++C+R A F +  SLLR  W +  +I+N+     ++ +  P   + 
Sbjct:   250 DMALDLRTVAHCSQLRCVRHAHFDVTDSLLRHAWHLPGIIKNLRQQRDIL-RAHPQLLRQ 308

Query:   311 QSVNMTDSD 319
             Q V +  +D
Sbjct:   309 QRVELRATD 317

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

ZFIN\|ZDB-GENE-040704-41 trub2 "TruB pseudouridine (psi) synthase homolog 2 (E. coli)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

MGI\|MGI:2442186 Trub2 "TruB pseudouridine (psi) synthase homolog 2 (E. coli)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1359394 Trub2 "TruB pseudouridine (psi) synthase homolog 2 (E. coli)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5XFW2 Trub2 "Probable tRNA pseudouridine synthase 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NEP1 TRUB2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|B7Z7G5 TRUB2 "cDNA FLJ52131, highly similar to Homo sapiens TruB pseudouridine (psi) synthase homolog 2 (TRUB2), mRNA" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RR98 TRUB2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RSQ5 TRUB2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|J9P6Q3 TRUB2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		336
cd02868		226	cd02868, PseudoU_synth_hTruB2_like, Pseudouridine	3e-37
cd00506		210	cd00506, PseudoU_synth_TruB_like, Pseudouridine sy	2e-13
cd02868		226	cd02868, PseudoU_synth_hTruB2_like, Pseudouridine	6e-10
pfam01509		149	pfam01509, TruB_N, TruB family pseudouridylate syn	2e-06
cd02573		213	cd02573, PseudoU_synth_EcTruB, Pseudouridine synth	1e-04
PRK05033		312	PRK05033, truB, tRNA pseudouridine synthase B; Pro	8e-04
PRK00130		290	PRK00130, truB, tRNA pseudouridine synthase B; Pro	0.001
COG0130		271	COG0130, TruB, Pseudouridine synthase [Translation	0.003
cd00506		210	cd00506, PseudoU_synth_TruB_like, Pseudouridine sy	0.004

>gnl\|CDD\|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase, humanTRUB2_like	Back alignment and domain information

 Score =  132 bits (335), Expect = 3e-37
 Identities = 45/106 (42%), Positives = 74/106 (69%)

Query: 188 RQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIR 247
               V   SQ+A ++A +G IRPA    P++YG++ + F+PP+FT+EV CI E +E+L +
Sbjct: 121 ELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFRPPEFTLEVQCINETQEYLRK 180

Query: 248 LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENI 293
           LI+++G +LRS+A+CT ++  R   F ++ +LLRK W +Q++I NI
Sbjct: 181 LIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQWNLQNIISNI 226

This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Length = 226

>gnl\|CDD\|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB family	Back alignment and domain information

>gnl\|CDD\|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase, humanTRUB2_like	Back alignment and domain information

>gnl\|CDD\|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal domain)	Back alignment and domain information

>gnl\|CDD\|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia coli TruB like	Back alignment and domain information

>gnl\|CDD\|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>gnl\|CDD\|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>gnl\|CDD\|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB family	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		336
PRK00130		290	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK14124		308	tRNA pseudouridine synthase B; Provisional	100.0
PRK04642		300	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK02755		295	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK01851		303	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK05389		305	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK01528		292	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK01550		304	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK05033		312	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK14123		305	tRNA pseudouridine synthase B; Provisional	100.0
TIGR00431		209	TruB tRNA pseudouridine 55 synthase. TruB, the tRN	100.0
PRK02484		294	truB tRNA pseudouridine synthase B; Provisional	100.0
cd02573		277	PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou	100.0
PRK03287		298	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK00020		244	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK14846		345	truB tRNA pseudouridine synthase B; Provisional	100.0
cd00506		210	PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo	100.0
PRK00989		230	truB tRNA pseudouridine synthase B; Provisional	100.0
cd02868		226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	100.0
PRK14122		312	tRNA pseudouridine synthase B; Provisional	100.0
PRK04099		273	truB tRNA pseudouridine synthase B; Provisional	100.0
PRK02193		279	truB tRNA pseudouridine synthase B; Provisional	100.0
cd02867		312	PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou	100.0
COG0130		271	TruB Pseudouridine synthase [Translation, ribosoma	100.0
PRK04270		300	H/ACA RNA-protein complex component Cbf5p; Reviewe	100.0
TIGR00425		322	CBF5 rRNA pseudouridine synthase, putative. This f	100.0
PF01509		149	TruB_N: TruB family pseudouridylate synthase (N te	100.0
cd02572		182	PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li	100.0
KOG2559\|consensus		318		99.94
cd02867		312	PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou	99.51
TIGR00431		209	TruB tRNA pseudouridine 55 synthase. TruB, the tRN	98.54
PF01509		149	TruB_N: TruB family pseudouridylate synthase (N te	98.53
KOG2559\|consensus		318		98.52
PRK00130		290	truB tRNA pseudouridine synthase B; Provisional	98.44
cd00506		210	PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo	98.43
PRK04099		273	truB tRNA pseudouridine synthase B; Provisional	98.42
PRK14124		308	tRNA pseudouridine synthase B; Provisional	98.4
PRK01851		303	truB tRNA pseudouridine synthase B; Provisional	98.4
cd02573		277	PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou	98.39
PRK02193		279	truB tRNA pseudouridine synthase B; Provisional	98.35
PRK00989		230	truB tRNA pseudouridine synthase B; Provisional	98.33
PRK00020		244	truB tRNA pseudouridine synthase B; Provisional	98.32
PRK05033		312	truB tRNA pseudouridine synthase B; Provisional	98.31
PRK05389		305	truB tRNA pseudouridine synthase B; Provisional	98.3
PRK02755		295	truB tRNA pseudouridine synthase B; Provisional	98.3
PRK01528		292	truB tRNA pseudouridine synthase B; Provisional	98.26
cd02868		226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	98.25
PRK14123		305	tRNA pseudouridine synthase B; Provisional	98.21
PRK14846		345	truB tRNA pseudouridine synthase B; Provisional	98.19
PRK02484		294	truB tRNA pseudouridine synthase B; Provisional	98.16
PRK14122		312	tRNA pseudouridine synthase B; Provisional	98.15
PRK01550		304	truB tRNA pseudouridine synthase B; Provisional	98.15
TIGR01213		388	conserved hypothetical protein TIGR01213. Members	98.12
PRK03287		298	truB tRNA pseudouridine synthase B; Provisional	98.09
PRK04642		300	truB tRNA pseudouridine synthase B; Provisional	98.07
PRK14554		422	putative pseudouridylate synthase; Provisional	97.89
KOG2529\|consensus		395		97.89
KOG2529\|consensus		395		95.42
COG1258		398	Predicted pseudouridylate synthase [Translation, r	94.6
cd02572		182	PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li	86.07
PRK04270		300	H/ACA RNA-protein complex component Cbf5p; Reviewe	84.1
COG0130		271	TruB Pseudouridine synthase [Translation, ribosoma	81.03

>PRK00130 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

Probab=100.00  E-value=3.1e-52  Score=398.50  Aligned_cols=196  Identities=16%  Similarity=0.308  Sum_probs=180.0

Q ss_pred             eeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceee
Q psy4559          70 VSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCV  148 (336)
Q Consensus        70 ~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI  148 (336)
                      .--|||+|+||||+       |+|+|||+++++.+.+ .+.....+|..|||.|..     |++..+             
T Consensus        34 ~GTLDP~AtGvL~v-------~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~D~~-----G~i~~~-------------   88 (290)
T PRK00130         34 TGTLDPLASGVLPV-------CLGKATKIVDYLMEGKKTYRAEIKLGVETDTYDRE-----GEILKE-------------   88 (290)
T ss_pred             CCCCCCCCeeEEEE-------EEChhhhhHHHhccCCcEEEEEEEECCcccCCCCC-----CCEEEe-------------
Confidence            34699999999999       9999999999999854 677777799999999995     887642             


Q ss_pred             eeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCCcceEEEEEEeeecC
Q psy4559         149 HFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKP  228 (336)
Q Consensus       149 ~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R~v~Iy~i~ll~~~~  228 (336)
                       ...++++.+++++++..|+|+++|+||         |  |||+|+||+|||||||+|++||+++|+|+||+|++++|+.
T Consensus        89 -~~~~~~t~~~l~~~l~~f~G~i~Q~PP---------~--ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~~~  156 (290)
T PRK00130         89 -KEVSHLTEEEIREAILSFQGEIDQVPP---------M--YSALKINGKKLYELARQGIEVEREARKITIYDIEILEIDL  156 (290)
T ss_pred             -cCCCCCCHHHHHHHHHHccCeEEEECC---------h--HHeEecCCHhHHHHHHCCCccccCceEEEEEEEEEEEEeC
Confidence             122358999999999999999999999         8  9999999999999999999999999999999999999999


Q ss_pred             CeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCChhHHHHHhhhhhhhhcccC
Q psy4559         229 PDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVDKMD  304 (336)
Q Consensus       229 p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~l~~I~~~i~~~~~lL~~~p  304 (336)
                      |.++|+|+||+|  |||||||||||.+|||+|||++||||++|+|++++|+++++|+.+++.+++.+++.+|.++|
T Consensus       157 ~~~~~~v~cskG--TYIRsL~~Dig~~Lg~~a~~~~LrRt~~G~f~~~~a~~l~~l~~~~~~~~l~p~~~~l~~lp  230 (290)
T PRK00130        157 PYVIFDVKCSKG--TYIRSLCFDIGEKLNCGAYMWNLIRTETGPFNIENSITLEDLNEENIEDYIIPIDKALKHYP  230 (290)
T ss_pred             CeEEEEEEECCC--CCHHHHHHHHHHHHCCCEEEEEEEeEEECCCCHHHcCCHHHHhhhhhhhhccCHHHHHhhCC
Confidence            999999999999  99999999999999999999999999999999999999999987777778888998887766

>PRK14124 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK04642 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02755 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01851 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05389 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01528 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01550 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05033 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14123 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>TIGR00431 TruB tRNA pseudouridine 55 synthase	Back alignment and domain information

>PRK02484 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like	Back alignment and domain information

>PRK03287 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK00020 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14846 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family	Back alignment and domain information

>PRK00989 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like	Back alignment and domain information

>PRK14122 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK04099 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02193 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4	Back alignment and domain information

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed	Back alignment and domain information

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative	Back alignment and domain information

>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones	Back alignment and domain information

>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like	Back alignment and domain information

>KOG2559\|consensus	Back alignment and domain information

>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4	Back alignment and domain information

>TIGR00431 TruB tRNA pseudouridine 55 synthase	Back alignment and domain information

>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones	Back alignment and domain information

>KOG2559\|consensus	Back alignment and domain information

>PRK00130 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family	Back alignment and domain information

>PRK04099 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14124 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01851 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like	Back alignment and domain information

>PRK02193 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK00989 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK00020 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05033 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05389 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02755 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01528 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like	Back alignment and domain information

>PRK14123 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14846 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02484 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14122 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01550 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>TIGR01213 conserved hypothetical protein TIGR01213	Back alignment and domain information

>PRK03287 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK04642 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14554 putative pseudouridylate synthase; Provisional	Back alignment and domain information

>KOG2529\|consensus	Back alignment and domain information

>KOG2529\|consensus	Back alignment and domain information

>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like	Back alignment and domain information

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed	Back alignment and domain information

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		336
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
1k8w_A		327	TRNA pseudouridine synthase B; protein-RNA complex	1e-05
1r3e_A		309	TRNA pseudouridine synthase B; RNA modification, p	1e-05
1sgv_A		316	TRNA pseudouridine synthase B; hinged motion, tRNA	8e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

 Score = 47.2 bits (111), Expect = 5e-06
 Identities = 52/350 (14%), Positives = 106/350 (30%), Gaps = 112/350 (32%)

Query: 13  ISMGDRLGPHVEAISGSTFSKDSWLKSQRKD----HKKIN-------------MTLLIKG 55
           IS+             S   K  +L  + +D        N                    
Sbjct: 289 ISLDHHSMTLTPDEVKSLLLK--YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346

Query: 56  WLSYMKNKKNITVLVSLIDL--------FVP-ALLPWQETVTVPSIKPLQKVLKIIDNNN 106
           W     +K    +  SL  L        F   ++ P   +  +P+      +L +I  + 
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP--PSAHIPT-----ILLSLIWFD- 398

Query: 107 CLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLP 166
                      +   +   V  +   + +L+++           K    +I ++Y     
Sbjct: 399 -----------VIKSDVMVVVNK-LHKYSLVEK---------QPKESTISIPSIY----- 432

Query: 167 WQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEP--------VV 218
             E  +K+ +   L      HR      N  + +D          L+           + 
Sbjct: 433 -LELKVKLENEYAL------HRSIVDHYNIPKTFD-------SDDLIPPYLDQYFYSHIG 478

Query: 219 YGLKCVHFKPPDFTIEVHCIGEYEEF-LIRLIY-D---LGTKLRSAAICTSIQCIRFAQF 273
           +     H K          I   E   L R+++ D   L  K+R  +   +      A  
Sbjct: 479 H-----HLKN---------IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN------ASG 518

Query: 274 GLEHSLLR-KHWRVQHVIENIAHNETLVDKMDPMRPQLQSVNMTDSDSTD 322
            + ++L + K ++  ++ +N    E LV+ +    P+++  N+  S  TD
Sbjct: 519 SILNTLQQLKFYK-PYICDNDPKYERLVNAILDFLPKIEE-NLICSKYTD 566

PyMOL of 1vt4

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Length = 327	Back alignment and structure

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Length = 309	Back alignment and structure

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Length = 316	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		336
1r3e_A		309	TRNA pseudouridine synthase B; RNA modification, p	100.0
1k8w_A		327	TRNA pseudouridine synthase B; protein-RNA complex	100.0
1sgv_A		316	TRNA pseudouridine synthase B; hinged motion, tRNA	100.0
2apo_A		357	Probable tRNA pseudouridine synthase B; protein-pr	100.0
3u28_A		400	H/ACA ribonucleoprotein complex subunit 4; pseudou	100.0
2aus_C		334	Pseudouridine synthase; isomerase, structural prot	100.0
2v9k_A		530	Uncharacterized protein FLJ32312; pseudouridine sy	98.41
1k8w_A		327	TRNA pseudouridine synthase B; protein-RNA complex	98.38
1r3e_A		309	TRNA pseudouridine synthase B; RNA modification, p	98.37
1sgv_A		316	TRNA pseudouridine synthase B; hinged motion, tRNA	98.28
2aus_C		334	Pseudouridine synthase; isomerase, structural prot	85.38
2apo_A		357	Probable tRNA pseudouridine synthase B; protein-pr	85.37
3u28_A		400	H/ACA ribonucleoprotein complex subunit 4; pseudou	81.36

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A	Back alignment and structure

Probab=100.00  E-value=4e-52  Score=399.24  Aligned_cols=216  Identities=14%  Similarity=0.180  Sum_probs=183.1

Q ss_pred             hhhhhhcCcceeEEeeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceee
Q psy4559          56 WLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRP  134 (336)
Q Consensus        56 ~~~~~~~~~~~~~~~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~  134 (336)
                      |+..+-+.|.+-- .--|||+|+||||+       |+|+|||+++++.+.. .|..+..+|..|||.|+.     |++..
T Consensus        22 ~vrr~l~~kKvGH-~GTLDP~AtGvL~i-------~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D~e-----G~v~~   88 (309)
T 1r3e_A           22 EVRKKLKTRKVGH-GGTLDPFACGVLII-------GVNQGTRILEFYKDLKKVYWVKMRLGLITETFDIT-----GEVVE   88 (309)
T ss_dssp             HHHHHTTCSCEEE-SSCCCTTCEEEEEE-------EEGGGGGGGGGGTTSCEEEEEEEEETEEESSSBTT-----SCEEE
T ss_pred             HHHHHhccceecc-cccCCCCcceeEEE-------EECHHHhHHHHhCccCcEEEEEEEECCcccCCCCC-----CCEEE
Confidence            3333333343333 45689999999999       9999999999998755 677777899999999995     88764


Q ss_pred             CCCCCceeecceeeeeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCC
Q psy4559         135 ALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLK  214 (336)
Q Consensus       135 t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R  214 (336)
                                     ..+..++.++|++++..|+|+|+|+||         |  |||+|+||||||||||+|++||+++|
T Consensus        89 ---------------~~~~~~t~~~i~~~l~~f~G~i~Q~PP---------~--~SAvKv~GkraYelAR~G~~ve~~~R  142 (309)
T 1r3e_A           89 ---------------ERECNVTEEEIREAIFSFVGEYDQVPP---------A--YSAKKYKGERLYKLAREGKIINLPPK  142 (309)
T ss_dssp             ---------------ECCCCCCHHHHHHHHHSSSEEEEECCC---------S--SSSCEETTEEHHHHHHTTCCCCCCCE
T ss_pred             ---------------EecCCCCHHHHHHHHHhccceEEEeCC---------h--HHhcccCCccHHHHHhCCCcccccce
Confidence                           233348999999999999999999999         8  99999999999999999999999999


Q ss_pred             cceEEEEEEeeecCCeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCChhHHHHHhh
Q psy4559         215 EPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIA  294 (336)
Q Consensus       215 ~v~Iy~i~ll~~~~p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~l~~I~~~i~  294 (336)
                      +|+||+|++++|+.|.|+|+|+||+|  |||||||||||++|||+|||++||||++|+|++++|+++++|....+.+.+.
T Consensus       143 ~v~I~~i~ll~~~~p~~~~~v~CskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~~a~~l~~l~~~~l~~~l~  220 (309)
T 1r3e_A          143 RVKIFKIWDVNIEGRDVSFRVEVSPG--TYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRII  220 (309)
T ss_dssp             EEEEEEEEEEEEETTEEEEEEEECTT--CCHHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGCBCTTTSCHHHHHHHCE
T ss_pred             EEEEEEEEEEEeeCCEEEEEEEECCC--chHHHHHHHHHHHhCCCEEEEEEEEEEEcCCcHHHccCHHHHhhchhhcccc
Confidence            99999999999999999999999999  9999999999999999999999999999999999999999997543434455


Q ss_pred             hhhhhhcccCCcCCCCceeeeCCCC
Q psy4559         295 HNETLVDKMDPMRPQLQSVNMTDSD  319 (336)
Q Consensus       295 ~~~~lL~~~p~~~~~l~~v~~~~~~  319 (336)
                      +++.+|.       .+|.+.++|++
T Consensus       221 p~~~~l~-------~~p~v~l~~~~  238 (309)
T 1r3e_A          221 PLEKCLE-------WLPRVVVHQES  238 (309)
T ss_dssp             EGGGSST-------TSCEEECCTTT
T ss_pred             CHHHHhc-------CCCeEEeCHHH
Confidence            5555554       45566655543

PyMOL of 1r3e

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A	Back alignment and structure

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A	Back alignment and structure

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A	Back alignment and structure

>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens}	Back alignment and structure

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A	Back alignment and structure

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A	Back alignment and structure

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A	Back alignment and structure

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		336
d1sgva2		233	d.265.1.2 (A:3-235) Pseudouridine synthase II TruB	4e-06
d1r3ea2		228	d.265.1.2 (A:10-237) Pseudouridine synthase II Tru	3e-04

>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 233	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 45.2 bits (106), Expect = 4e-06
 Identities = 20/118 (16%), Positives = 44/118 (37%), Gaps = 6/118 (5%)

Query: 166 PWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVH 225
              EA+    +     +       + +++  + AY +ARQG       +   +   + + 
Sbjct: 96  LTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLA 155

Query: 226 FKP----PDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
            +      D  +E+ C      ++  L  DLG  L      T+++  R  +F L+ + 
Sbjct: 156 ARRRDQLIDIDVEIDCSSGT--YIRALARDLGDALGVGGHVTALRRTRVGRFELDQAR 211

PyMOL of d1sgva2

>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Length = 228	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		336
d1r3ea2		228	Pseudouridine synthase II TruB {Thermotoga maritim	100.0
d1k8wa5		242	Pseudouridine synthase II TruB {Escherichia coli [	100.0
d1sgva2		233	Pseudouridine synthase II TruB {Mycobacterium tube	100.0
d2apoa2		230	Pseudouridine synthase II TruB {Archaeon Methanoco	100.0
d2ey4a2		245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	100.0
d1r3ea2		228	Pseudouridine synthase II TruB {Thermotoga maritim	98.26
d1sgva2		233	Pseudouridine synthase II TruB {Mycobacterium tube	98.21
d1k8wa5		242	Pseudouridine synthase II TruB {Escherichia coli [	98.06

>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Thermotoga maritima [TaxId: 2336]

Probab=100.00  E-value=5.3e-50  Score=367.48  Aligned_cols=193  Identities=15%  Similarity=0.193  Sum_probs=180.1

Q ss_pred             eeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceee
Q psy4559          70 VSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCV  148 (336)
Q Consensus        70 ~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI  148 (336)
                      .--|||+|+||||+       |+|++||+++++.+.+ .+.....+|..|||.|..     |++..              
T Consensus        35 ~GTLDP~AsGvL~i-------~ig~~tkl~~~~~~~~K~Y~~~~~lG~~TdT~D~~-----G~i~~--------------   88 (228)
T d1r3ea2          35 GGTLDPFACGVLII-------GVNQGTRILEFYKDLKKVYWVKMRLGLITETFDIT-----GEVVE--------------   88 (228)
T ss_dssp             SSCCCTTCEEEEEE-------EEGGGGGGGGGGTTSCEEEEEEEEETEEESSSBTT-----SCEEE--------------
T ss_pred             CcccCCcceeeEEE-------EEcccccchhhhhcccceEEEEEEEeccccccccC-----Cccce--------------
Confidence            44599999999999       9999999999998866 688888899999999995     87653              


Q ss_pred             eeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCCcceEEEEEEeeecC
Q psy4559         149 HFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKP  228 (336)
Q Consensus       149 ~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R~v~Iy~i~ll~~~~  228 (336)
                       ......+.++|+++|..|+|.+.|.||         +  |||+|+||+|||||||+|+.+++++|+|.||++++++++.
T Consensus        89 -~~~~~~~~~~i~~~l~~f~G~~~Q~pP---------~--ySA~Kv~Gkr~Y~lAR~g~~~~~~~r~v~I~~~~l~~~~~  156 (228)
T d1r3ea2          89 -ERECNVTEEEIREAIFSFVGEYDQVPP---------A--YSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEG  156 (228)
T ss_dssp             -ECCCCCCHHHHHHHHHSSSEEEEECCC---------S--SSSCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEEET
T ss_pred             -ecccchhHHHHHHHHHhccChhhhHHH---------H--HHHhhcchHHHHHHHHhhhccccccchhhhhhhhheeecC
Confidence             234456889999999999999999999         7  9999999999999999999999999999999999999999


Q ss_pred             CeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCChhHHHHHhhhhhhhhcc
Q psy4559         229 PDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVDK  302 (336)
Q Consensus       229 p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~l~~I~~~i~~~~~lL~~  302 (336)
                      |.++|+|+||+|  |||||||||||.+|||+|||++||||++|+|++++|++++++..+++.+++.|++++|+|
T Consensus       157 ~~~~~~v~cs~G--TYIRsL~~dlg~~Lg~~a~l~~LrR~~~G~f~l~~a~~l~~~~~~~i~~~i~P~e~~L~~  228 (228)
T d1r3ea2         157 RDVSFRVEVSPG--TYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEW  228 (228)
T ss_dssp             TEEEEEEEECTT--CCHHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGCBCTTTSCHHHHHHHCEEGGGSSTT
T ss_pred             CcceeEEEECCH--HHHHHHHHHHHHHcCCcEEEeEeEEeeecCcChHHcCCHHHhCHhHHHhhhcCHHHHhCc
Confidence            999999999999  999999999999999999999999999999999999999999999999999999999865

PyMOL of d1r3ea2

>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]}	Back information, alignment and structure